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1. Overview of Amino Acid Oxidation and Urea Cycle Amino Acids: Nitrogen-containing macromolecules crucial for protein synthesis and metabolic energy generation. Amino Acid Catabolism: Breakdown of amino acids, contributing to metabolic energy. Energy Sources: Car...

1. Overview of Amino Acid Oxidation and Urea Cycle Amino Acids: Nitrogen-containing macromolecules crucial for protein synthesis and metabolic energy generation. Amino Acid Catabolism: Breakdown of amino acids, contributing to metabolic energy. Energy Sources: Carnivores use up to 90% of energy from amino acids, while herbivores and plants rely on other sources, primarily glucose. 2. Conditions Leading to Amino Acid Catabolism Amino acid catabolism occurs under three major conditions: 1. Protein Synthesis: During normal breakdown and synthesis of proteins. 2. Protein-Rich Diet: Surplus amino acids undergo catabolism (since amino acids cannot be stored). 3. Starvation or Diabetes: Body proteins are used for energy. 3. Fate of Amino Acids Amino Groups: The α-amino group of amino acids is removed and either converted to urea or incorporated into other compounds. The carbon skeleton is converted into intermediates like acetyl-CoA, pyruvate, or citric acid cycle intermediates. Site of Degradation: The liver is the major site for amino acid degradation. Excess Nitrogen: Excess nitrogen from amino acids is converted into urea and excreted. 4. Digestive Breakdown of Dietary Protein Gastrin: Secreted by the stomach, stimulates hydrochloric acid (HCl) and pepsinogen secretion. o Pepsin: Activates to degrade proteins, cleaving at aromatic amino acids. Secretin: Stimulates pancreatic bicarbonate secretion and bile release from the gallbladder. Pancreatic Enzymes: o Trypsin: Activated from trypsinogen, cleaves proteins at lysine and arginine residues. 5. The Amino Acid Pool Protein Degradation: After digestion and absorption, amino acids enter the amino acid pool for: o Synthesis of Non-Essential Amino Acids. o Non-Protein Nitrogen Compounds (e.g., porphyrins, creatine, hormones, neurotransmitters). o Protein Synthesis.  Energy Generation: Catabolism leads to a loss of nitrogen, necessitating dietary intake to replenish the amino acid pool. 6. Key Steps in Amino Acid Catabolism Transamination: Transfer of an amino group from an amino acid to an α-keto acid. o Example: Amino group from an amino acid is transferred to α-ketoglutarate, forming glutamate. o Enzyme: Catalyzed by transaminases (aminotransferases) with pyridoxal phosphate (PLP) as a cofactor. Deamination: Removal of amino groups as free ammonia (NH₃). o Oxidative Deamination: Occurs primarily with glutamate, yielding ammonia and α-ketoglutarate. This is catalyzed by glutamate dehydrogenase in the mitochondria. o Non-Oxidative Deamination: Occurs with amino acids like serine, threonine, catalyzed by PLP-dependent dehydratases. 7. Ammonia Metabolism and Transport Toxicity of Ammonia: Ammonia is highly toxic, so it must be efficiently converted into non-toxic compounds. Transport Forms: o Glutamine: Ammonia is captured by glutamine synthetase in various tissues (liver, kidney, brain), forming glutamine, which is non-toxic and transported to the liver. o Alanine: The glucose-alanine cycle transfers ammonia in alanine form from muscle to the liver. 8. The Urea Cycle (Krebs-Henseleit Cycle) Goal: Convert toxic ammonia to urea for excretion. Location: Occurs in liver mitochondria and cytosol. Steps in Urea Cycle: 1. Carbamoyl Phosphate Synthetase I: Captures free ammonia to form carbamoyl phosphate (rate-limiting step). 2. Ornithine Transcarbamoylase: Converts carbamoyl phosphate to citrulline. 3. Argininosuccinate Synthase: Combines citrulline with aspartate to form argininosuccinate. 4. Argininosuccinase: Cleaves argininosuccinate to produce arginine and fumarate. Fumarate enters the citric acid cycle. 5. Arginase: Cleaves arginine to produce urea and regenerate ornithine, completing the cycle. 9. The “Krebs Bicycle” The urea cycle and citric acid cycle are interconnected: o Fumarate from the urea cycle enters the citric acid cycle. o Aspartate formed in the citric acid cycle contributes to the urea cycle, creating a feedback loop. 10. Regulation of Urea Cycle Carbamoyl Phosphate Synthetase I is the key regulatory enzyme, controlling the rate of urea cycle activity. Increased Protein Catabolism: Leads to increased production of ammonia, activating the urea cycle. 11. Nitrogen Excretion Excretion Forms: 1. Ammonia: Excreted by aquatic vertebrates (ammonotelic animals). 2. Urea: Excreted by terrestrial vertebrates and humans (ureotelic animals). 3. Uric Acid: Excreted by birds, reptiles (uricotelic animals). 12. Role of Glutamate in Nitrogen Metabolism Glutamate acts as a central amino group collector, undergoing oxidative deamination to release ammonia and form α-ketoglutarate, which enters the citric acid cycle. Glutamine: A transport form of ammonia, which is converted back to glutamate in the liver, releasing ammonia for urea synthesis. Key Takeaways: Amino acid catabolism is essential for energy production, especially in protein-rich diets or during starvation. Ammonia is toxic, requiring conversion to non-toxic urea via the urea cycle in the liver. The glucose-alanine cycle and glutamine transport are key for safe ammonia transport from muscles and peripheral tissues to the liver. Transamination and deamination are central processes for amino acid breakdown. Urea Cycle: The urea cycle (or Krebs-Henseleit cycle) is a metabolic pathway that converts toxic ammonia, produced from the breakdown of amino acids, into urea for excretion. It occurs primarily in the liver and involves the following key steps: 1. Carbamoyl Phosphate Synthesis: Ammonia combines with bicarbonate to form carbamoyl phosphate (using ATP). 2. Citrulline Formation: Carbamoyl phosphate reacts with ornithine to form citrulline. 3. Argininosuccinate Synthesis: Citrulline combines with aspartate (providing nitrogen) to form argininosuccinate. 4. Cleavage of Argininosuccinate: Argininosuccinate is split into arginine and fumarate. 5. Urea Formation: Arginine is converted to urea, releasing ornithine to start the cycle again. The cycle's main purpose is to detoxify ammonia by converting it into urea, which can then be safely excreted by the kidneys. Krebs Bicycle: The Krebs Bicycle describes the interconnectedness between the urea cycle and the citric acid cycle (Krebs cycle). Both cycles share intermediates, particularly fumarate, which is produced in the urea cycle and then enters the citric acid cycle. This interplay allows both nitrogen detoxification and energy production to occur simultaneously: Fumarate from the urea cycle enters the citric acid cycle, where it's converted to malate and then oxaloacetate, which is essential for energy production. The urea cycle helps eliminate excess nitrogen (from amino acid breakdown), while the citric acid cycle generates ATP for the cell's energy needs. In essence, the Krebs Bicycle is the efficient metabolic coupling of the two cycles, balancing nitrogen waste disposal and energy production. LECTURE 8. Important Notes (NB) on Slide 2: Nucleosides vs. Nucleotides: o Nucleosides: Composed of a sugar (ribose or deoxyribose) and a base (purine or pyrimidine). o Nucleotides: Nucleosides with an added phosphate group (one, two, or three phosphates attached). o Phosphate adds energy and enables nucleotides to be used in DNA/RNA synthesis, energy transfer (ATP, GTP), and regulation. Key takeaway: Nucleotides are the active forms, crucial for cellular functions. 2. What is needed to form CAIR (as per slide 43)?  CAIR (5'-phosphoribosyl-5-aminoimidazole-4-carbonate) is a key intermediate in purine biosynthesis. o Precursors for CAIR: § Ribose-5-phosphate (from pentose phosphate pathway). § Glutamine (provides nitrogen). § Glycine, tetrahydrofolate (THF), and bicarbonate contribute carbon atoms and energy for ring formation. o Energy requirement: Requires ATP in multiple steps to form the purine ring. Important to remember: The pathway from PRPP to CAIR is a critical step in purine synthesis. 3. Focus on Gout (Hint) Gout is caused by the accumulation of uric acid (a byproduct of purine metabolism) in tissues, leading to inflammation and pain. Key to remember: o Purines are broken down into uric acid, and high levels can result in gout. o Gout is often linked to an overproduction of purines or impaired excretion of uric acid. o Medications for gout may target the enzyme xanthine oxidase, which catalyzes the final step of purine degradation. 4. Focus on the First Two Nucleotide Metabolism Pathways: Purine Synthesis (De Novo Pathway): Starts with PRPP: PRPP is the key intermediate in purine biosynthesis. o Enzyme: PRPP synthetase (adds pyrophosphate group to ribose). o Glutamine donates ammonia to form 5-phosphoribosyl-1-amine. o ATP and GTP provide energy for subsequent steps in purine ring formation. Key intermediate: IMP (Inosine Monophosphate). o IMP is the precursor for both AMP (Adenosine Monophosphate) and GMP (Guanosine Monophosphate). o GMP is synthesized via xanthosine and glutamine (requires ATP). o AMP is synthesized via fumarate and aspartate (requires GTP). Remember: IMP is a common intermediate, and GTP is used for AMP, while ATP is used for GMP. Pyrimidine Synthesis (De Novo): Begins with carbamoyl phosphate formed by glutamine, bicarbonate, and ATP. o Formed in the cytoplasm (distinct from urea cycle). o Reacts with aspartate to form carbamoyl aspartate. o Cyclization leads to the formation of orotate, which reacts with PRPP to form OMP (orotidine monophosphate).  Uridine (UMP) is then formed from OMP, and UTP is formed via phosphorylation. o CTP is formed by adding an amino group to UTP. Key takeaway: Pyrimidine biosynthesis starts with a simpler structure (the 6-membered ring), and PRPP is involved. 5. Know the Essential and Non-Essential Amino Acids: Essential Amino Acids: These must be obtained from the diet. The body cannot synthesize them. Examples: o Histidine, Valine, Leucine, Isoleucine, Lysine, Methionine, Phenylalanine, Threonine, Tryptophan, Arginine (conditionally essential in some situations). Non-Essential Amino Acids: These can be synthesized by the body. Examples: o Glutamate, Glutamine, Aspartate, Alanine, Serine, Tyrosine (from phenylalanine), Cysteine (from methionine), Proline, Asparagine. Remember: Essential amino acids must be consumed in the diet, while non-essential amino acids can be synthesized in the body. 6. Know the Amphibolic Amino Acids: Amphibolic amino acids: These are amino acids that can be used to generate both glucose (via gluconeogenesis) and ketone bodies (via ketogenesis), meaning they can be either glucogenic or ketogenic. Examples: o Phenylalanine, Isoleucine, Threonine, Tryptophan, Tyrosine. Key takeaway: Amphibolic amino acids are important because they can serve as precursors for energy production pathways depending on the body's needs. 7. Precursor Relationships for Amino Acids (Slide 43): Histidine comes from ribose 5-phosphate (a PPP product). Serine comes from 3-phosphoglycerate (glycolytic intermediate). Tryptophan and Tyrosine come from phosphoenolpyruvate (a glycolytic intermediate). Pyruvate is used to make alanine, valine, leucine, and isoleucine. Remember: Many amino acids are derived from central metabolic intermediates like pyruvate, 3-phosphoglycerate, and phosphoenolpyruvate. 8. Biosynthetic Pathways for Purines and Pyrimidines: Purine Pathway: Starting compound: PRPP. Key intermediates: CAIR, IMP. Energy sources: ATP, GTP. Regulation: Purine synthesis is regulated by AMP and GMP (feedback inhibition). Pyrimidine Pathway: Starting compound: Carbamoyl phosphate (from glutamine, bicarbonate, and ATP). Key intermediates: UMP, UTP, CTP. Energy sources: ATP. Regulation: CTP feedback inhibits the synthesis of carbamoyl phosphate. Takeaway: Purine synthesis is more complex (requires both ATP and GTP), while pyrimidine synthesis starts from a simpler 6-membered ring structure. Quick Recap: Purine synthesis starts with PRPP, progresses through IMP, and forms AMP and GMP. Pyrimidine synthesis starts with carbamoyl phosphate and forms UMP, UTP, and CTP. Essential amino acids must come from the diet; non-essential amino acids can be synthesized by the body. Amphibolic amino acids can be both glucogenic and ketogenic.